Surface functionalization and pore filling of porous layers are essential key aspects for successful application of complex porous matrices. Atomic layer deposition (ALD) in deep macroporous trenches with high aspect ratio using different coating materials was investigated for a wide field of applications, such as energy storage, catalysis, and membrane technology1-3. Experimental data for ALD into mesopores, especially in the low mesoporous range (up to 20 nm) are rare4, 5. ALD on and into mesoporous silicon layers has different functions: 1st Surface passivation (sealing) of the underlying mesoporous structures, such as electrical barrier, diffusion barrier or corrosion protection. In this case complete pore filling is necessary to avoid transport processes through the passivated mesoporous interface. 2nd Pore size reduction (narrowing), i.e. adjustment of pore size for mesoporous membranes or single pores, e.g. for universally applicable, label-free, and nanopore-based sensor systems for the detection of small molecules in the nanofiltration range. Additionally, pore narrowing can be used for fine tuning of porous silicon-based sensors or optical filter properties5. 3rd Surface functionalization, e.g. in biomimetic or bioinspired systems or in fuel cells as catalytic layer.This contribution gives an extensive investigation of single and multi-layer depositions on and into mesoporous silicon layers and analyzes the material distribution and penetration profile of the corresponding atomic compositions.Mesoporous silicon layers were fabricated using highly doped (0.01-0.02 Ωcm) p-type substrates. Electrochemical etching (anodization) was performed in a mixture of 50 m% HF and absolute ethanol in volume ratio 1:1, to generate a 5 µm thick mesoporous layer. A current density of 70 mA/cm2 was used. 48 % porosity was measured by gravimetric technique. Nitrogen adsorption-desorption isotherms were measured in a Belsorp-mini from Rubotherm/Bel GmbH at 77 K using native porous silicon layers. Pore radius (rp) and pore radius distribution were evaluated using Barrett-Joyner-Halenda (BJH) theory. An average pore size radius of 4.68 nm, and pore radius range up to 12 nm were measured. However, surface oxidation will change the layer morphology, especially the pore size, porosity, and specific surface area.The layer deposition process was carried out with different ALD single layers, such as thermal Al2O3, plasma TiO2, thermal HfO2, thermal ZnO, and layer combinations as multilayer ALD, such as plasma Al2O3/TiO2 in an Oxford FlexAl reactor. Typical ALD cycle consists of two half-cycles, sequential precursor and co-reactant doses, which are separated by purge and pump steps, leading to self-limited layer growth6. Co-reactants and oxidizers are typically oxygen sources (H2O or oxygen plasma). When using an oxygen-containing medium, vacuum oxidation occurs, which leads to partial oxidation of the huge inner surface of the mesoporous layer5.Characterization of ultrathin layer deposited in complex 3D mesoporous structures is challenging and demands special analysis methods. In our experiments the penetration depth and depth distributions of atomic compositions for different ALD single and multilayers were measured using secondary neutral mass spectrometry (SNMS). Fig. 1 shows one example of the material distribution for Al2O3 atomic compositions on silicon substrate (Fig. 1a) and on and into mesoporous silicon substrate (Fig. 1b) with the same nominal Al2O3 layer thickness of 96.89 nm, which was measured on the silicon substrate with a Woollan M-2000FTM ellipsometer. The influence of both half-cycles of the ALD process must be considered at the evaluation, both the deposition effect on and into mesoporous silicon layers, and the transformation of the inner pore surface by oxidation. In the mesoporous layer the Al atomic composition profile follows the initial Al atomic profile up to 110 nm and subsequently shows a decreasing tendency up to 225 nm. The O atomic composition shows a decreasing tendency from 125 nm to 225 nm, and a saturation at 3.5 atomic percent. The existence of O in the deeper (>250 nm) mesoporous layers (Fig. 1b) indicates the partial oxidation of the underlying mesoporous layer occurring mainly during the H2O dose half-cycle process sequence. Penetration depths and profiles will be presented for the investigated single ALD layer. Further experimental results show that for multilayer ALD, e.g. with Al2O3/TiO2 layer combination, the first ALD-layer of the multilayer and its specific properties are dominating in the pore filling of the mesoporous layer.